@rcsb/rcsb-search-tools 0.0.1

package/README.md

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+# rcsb-search-tools
+
+RCSB Search Tools is an open-source library that includes different tools to build queries, request and parse data from the 
+[RCSB Search API](https://search.rcsb.org/).
+
+### Node Module Instalation
+`npm install @rcsb/rcsb-search-tools`
+
+### Folder organization
+- `src` module source code
+  - `SearchClient` RCSB Search API client 
+  - `SearchQueryTools` Tools for building search requests
+  - `SearchParseTools` Tools for parsing RCSB Search API responses
+- `test` Unit tests
+
+### Examples
+
+Multiple examples can be found in the `test` folder as part of unit tests

package/lib/SearchClient/SearchClient.js

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+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.SearchClient = void 0;
+const SearchRequest_1 = require("@rcsb/rcsb-api-tools/build/RcsbSearch/SearchRequest");
+class SearchClient {
+    static get() {
+        return this.client;
+    }
+    static set(client) {
+        this.client = client;
+    }
+}
+SearchClient.client = new SearchRequest_1.SearchRequest();
+exports.SearchClient = SearchClient;

package/lib/SearchFacetTools/SearchFacetInterface.js

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+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });

package/lib/SearchFacetTools/SearchFacetTools.js

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+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.getFacetsFromSearch = void 0;
+function getFacetsFromSearch(searchResult) {
+    if (!searchResult.facets)
+        return [];
+    return getBucketsFromFacets(searchResult.facets);
+}
+exports.getFacetsFromSearch = getFacetsFromSearch;
+function getBucketsFromFacets(searchResultFacets, labelList, recursiveOut) {
+    const out = recursiveOut !== null && recursiveOut !== void 0 ? recursiveOut : [];
+    const facets = collectFacets(searchResultFacets);
+    facets.forEach(bucketFacet => {
+        const innerFacets = bucketFacet.buckets.filter(g => Array.isArray(g.facets));
+        if (innerFacets.length > 0) {
+            innerFacets.forEach(g => {
+                if (g.facets)
+                    getBucketsFromFacets(g.facets, labelList ? labelList.concat(g.label) : [g.label], out);
+            });
+        }
+        const searchBucketFacet = {
+            name: bucketFacet.name,
+            labelPath: labelList !== null && labelList !== void 0 ? labelList : [],
+            data: []
+        };
+        bucketFacet.buckets.forEach(bucket => {
+            if (bucket.label && bucket.population)
+                searchBucketFacet.data.push({
+                    label: bucket.label,
+                    population: bucket.population
+                });
+        });
+        out.push(searchBucketFacet);
+    });
+    return out;
+}
+function collectFacets(facets) {
+    return facets.map(f => ('value' in f ? {
+        name: f.name,
+        buckets: [{
+                label: f.name,
+                population: f.value
+            }]
+    } : f));
+}

package/lib/SearchQueryTools/SearchQueryInterfaces.js

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+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });

package/lib/SearchQueryTools/SearchQueryTools.js

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+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.buildAttributeQuery = exports.combineSearchQuery = exports.addAttributeToSearchQuery = exports.buildRequestFromSearchQuery = exports.buildRequestFromCombinedSearchQuery = exports.buildRequestFromAttributeAndSearchQuery = exports.buildRequestFromAttribute = void 0;
+const SearchEnums_1 = require("@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchEnums");
+const lodash_1 = require("lodash");
+function buildRequestFromAttribute(searchAttribute, returnType, requestOptions) {
+    return {
+        query: buildAttributeQuery(searchAttribute),
+        return_type: returnType,
+        request_options: requestOptions
+    };
+}
+exports.buildRequestFromAttribute = buildRequestFromAttribute;
+function buildRequestFromAttributeAndSearchQuery(searchAttribute, searchQuery, returnType, logicalOperator = SearchEnums_1.LogicalOperator.And, requestOptions) {
+    return {
+        query: addAttributeToSearchQuery(searchAttribute, searchQuery, logicalOperator),
+        return_type: returnType,
+        request_options: requestOptions
+    };
+}
+exports.buildRequestFromAttributeAndSearchQuery = buildRequestFromAttributeAndSearchQuery;
+function buildRequestFromCombinedSearchQuery(additionalSearchQuery, searchQuery, returnType, logicalOperator = SearchEnums_1.LogicalOperator.And, requestOptions) {
+    return {
+        query: combineSearchQuery(additionalSearchQuery, searchQuery),
+        return_type: returnType,
+        request_options: requestOptions
+    };
+}
+exports.buildRequestFromCombinedSearchQuery = buildRequestFromCombinedSearchQuery;
+function buildRequestFromSearchQuery(searchQuery, returnType, requestOptions) {
+    return {
+        query: searchQuery,
+        return_type: returnType,
+        request_options: requestOptions
+    };
+}
+exports.buildRequestFromSearchQuery = buildRequestFromSearchQuery;
+function addAttributeToSearchQuery(searchAttribute, searchQuery, logicalOperator = SearchEnums_1.LogicalOperator.And) {
+    return combineSearchQuery(buildAttributeQuery(searchAttribute), searchQuery, logicalOperator);
+}
+exports.addAttributeToSearchQuery = addAttributeToSearchQuery;
+function combineSearchQuery(additionalSearchQuery, searchQuery, logicalOperator = SearchEnums_1.LogicalOperator.And) {
+    if (searchQuery.type === SearchEnums_1.Type.Group && searchQuery.logical_operator === logicalOperator) {
+        const query = (0, lodash_1.cloneDeep)(searchQuery);
+        query.nodes.push(additionalSearchQuery);
+        return query;
+    }
+    return {
+        type: SearchEnums_1.Type.Group,
+        logical_operator: logicalOperator,
+        nodes: [
+            searchQuery,
+            additionalSearchQuery
+        ]
+    };
+}
+exports.combineSearchQuery = combineSearchQuery;
+function buildAttributeQuery(searchAttribute) {
+    return {
+        type: SearchEnums_1.Type.Terminal,
+        service: searchAttribute.service,
+        parameters: {
+            attribute: searchAttribute.attribute,
+            negation: typeof searchAttribute.negation === "boolean" ? searchAttribute.negation : false,
+            operator: searchAttribute.operator,
+            value: searchAttribute.value
+        }
+    };
+}
+exports.buildAttributeQuery = buildAttributeQuery;

package/package.json

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+{
+  "name": "@rcsb/rcsb-search-tools",
+  "version": "0.0.1",
+  "description": "RCSB PDB Search API request tools",
+  "main": "build/app.js",
+  "files": [
+    "lib"
+  ],
+  "scripts": {
+    "test": "jest",
+    "tsc": "tsc",
+    "publishApp": "npm publish"
+  },
+  "repository": {
+    "type": "git",
+    "url": "git://github.com/rcsb/rcsb-search-tools.git"
+  },
+  "publishConfig": {
+    "registry": "https://registry.npmjs.org/"
+  },
+  "author": "Joan Segura Mora",
+  "license": "MIT",
+  "devDependencies": {
+    "@babel/core": "^7.18.9",
+    "@babel/preset-env": "^7.18.9",
+    "@types/jest": "^29.5.1",
+    "@types/lodash": "^4.14.194",
+    "@types/node-fetch": "^2.6.2",
+    "babel-loader": "^9.1.2",
+    "jest": "^29.5.0",
+    "lodash": "^4.17.21",
+    "node-fetch": "^2.6.7",
+    "ts-jest": "^29.1.0",
+    "ts-loader": "^9.3.1",
+    "ts-node": "^10.9.1",
+    "typescript": "^5.0.4",
+    "webpack": "^5.74.0",
+    "webpack-cli": "^5.1.1"
+  },
+  "dependencies": {
+    "@rcsb/rcsb-api-tools": "^4.1.5"
+  }
+}